PRODIGY

NAME

prodigy - binding affinity predictor

DESCRIPTION

usage: prodigy [-h] [--distance-cutoff DISTANCE_CUTOFF]

[--acc-threshold ACC_THRESHOLD] [--temperature TEMPERATURE] [--contact_list] [--pymol_selection] [-q] [-V] [--selection A B [A,B C ...]] structf

Binding affinity predictor based on Intermolecular Contacts (ICs).

Anna Vangone and Alexandre M.J.J. Bonvin, Contacts-based prediction of binding affinity in protein-protein complexes. eLife (2015)

positional arguments:

structf

Structure to analyse in PDB or mmCIF format

options:

-h, --help

show this help message and exit

--distance-cutoff DISTANCE_CUTOFF

Distance cutoff to calculate ICs

--acc-threshold ACC_THRESHOLD

Accessibility threshold for BSA analysis

--temperature TEMPERATURE

Temperature (C) for Kd prediction

--contact_list

Output a list of contacts

--pymol_selection

Output a script to highlight the interface (pymol)

-q, --quiet

Outputs only the predicted affinity value

-V, --version

Print the version and exit.

Selection Options:

By default, all intermolecular contacts are taken into consideration, a molecule being defined as an isolated group of amino acids sharing a common chain identifier. In specific cases, for example antibody-antigen complexes, some chains should be considered as a single molecule.

Use the --selection option to provide collections of chains that should be considered for the calculation. Separate by a space the chains that are to be considered _different_ molecules. Use commas to include multiple chains as part of a single group:

--selection A B => Contacts calculated (only) between chains A and B.

--selection A,B C => Contacts calculated (only) between

chains A and C; and B and C.

--selection A B C => Contacts calculated (only) between

chains A and B; B and C; and A and C.

--selection A B [A,B C ...]